I've just refreshed my memory... had a look at the user guide. There's no mention of that facilities file because it's maintain buy the 'Add a new facility' feature in PF3, which you access from Options #2.
The section to check in the user guide is
7.1.21 Add a New Facility Frequency or mark Airport Closed although the actual section number may have changed since I'v been doing a lot of work with the guide.
Here's the part I saw which refreshed my memory, as the change was made in April 2017 !!
Since PF3 3.4.0 there is a new feature which allows you to 'virtually' remove
an FS facility. If, for instance, you select EGSS, which has two Tower
frequencies in the default FS9, and enter a frequency of 137 against 'Tower',
when you start your flight the COMS display will show that the Tower at EGSS
is no longer available. This allows you to basically remove any facility for any
airport.
Because PF3 does not allow duplicate frequencies you need to make each
137 frequency unique if you wish to remove more than one facility per
airport. eg. 137.02, 137.05, etc.
You cannot remove the ATIS, Departure or FSS facilities and we do not make
any alterations to FS at all, this is merely a mask whilst PF3 is running.
So I guess sometime back in 2020 you did use this feature to remove some facilities from EDDP and that's where the 137 frequencies came from.